Rio de Janeiro was chosen by acclamation by the Brazilian Olympic Committee (BOC) as the national applicant city for the XXXI Olympiad on September 1, 2006, starting a process of ten years until the Olympics.^[46] This is the first time that the city has proceeded to the Candidature phase, after four failed attempts in 1936, 1940, 2004 and 2012.^[47] Rio would become the first Brazilian and South American city to host the games.^[48] Rio de Janeiro planned to perform all the competitions inside the city, bringing dynamics to the games and facilitating the athlete's interaction.^[49] There will be seven competition centers in four Olympic regions—Barra, Copacabana, Deodoro, and Maracanã—^[50] where football matches will be held in the cities of Belo Horizonte, Brasília, Salvador and São Paulo.^[51] The proposed dates range from August 5 to August 21 for the Summer Olympic Games, and September 7 (Independence Day of Brazil) to September 18 for the Summer Paralympic Games.^[49] Rio de Janeiro failed in the previous applications mainly by lack of infrastructure, security and experience in organization of international sporting events. Brazil hosted the 1950 FIFA World Cup, where Rio was one of the host cities and place of the final match, but the structures have been deteriorating over time despite several reforms. However, the XV Pan American Games, held in Rio de Janeiro between July 13 and July 29, 2007, changed the idea of failure of the city.^[52] The event was considered the best in history by the president of the Pan American Sports Organisation (PASO), Mario Vazquez Raña, during his speech at the closing ceremony.^[53] Brazil later organized the FIFA World Cup in 2014, adding more experience to Rio, which hosted the final match for the second time.^[54] According to the ROCOG, the entire city would to be transformed into a theater for the occasion.^[49] The compact footprint, complemented by Rio's topography, involves seven competition clusters in four Olympic zones—Barra, Copacabana, Deodoro, and Maracanã—, all held within the city. At the heart of the concept is the Barra zone, located in one of the newer and fastest growing regions of the city, framed by mountains, beaches and lagoons.^[55] The logo was revealed on December 17, 2007, during the Brazil's Olympic Award ceremony at the Municipal Theater of Rio de Janeiro, and was selected by a jury from among four finalists.^[56] The BOC chose the Sugarloaf Mountain (Portuguese: Pão de Açucar), a prominent landmark of the city, as their symbol.^[57] This landscape results in a heart shape that, in its turn, represents the Brazilian's unquestionable passion and enthusiasm for sports.^[57]

The same day London was chosen for organizing the 2012 Summer Olympics, the mayor of Madrid spoke of an interest to make a bid for the 2016 games.Considering its strong showing in the 2012 bidding, one year later, the city council unanimously voted for the submission of a new bid. In May 2007, mayor Alberto Ruiz-Gallardón filed with the Spanish Olympic Committee (COE, Spanish: Comité Olímpico Español) as the only Spanish internal candidate for the Games.^[58] The Spanish Field Hockey Federation vice-chairwoman Mercedes Coghen was chosen as chairwoman of the project. Former IOC president Juan Antonio Samaranch offered his help in this new attempt. Madrid benefited from its strong reputation from the 2012 bid as well as having 85% of venues in place and many experiences hosting Olympic qualifying events.^[59] Later plans stressed two clusters of venues, one on the east side, the other along the Manzanares River.^[60] The bid was also popular with the Madrileños, boasting 85% support and 60% believing they could win the bid.^[61] One potential problem was that no continent has hosted successive Summer Games since the special circunstances who led Helsinki to host the 1952 Summer Olympics followed London as 1948 Summer Olympics host city. London was scheduled to host the 2012 Summer Olympics, and Athens, Greece fielded the 2004 Summer Olympics. Furthermore, the 2014 Winter Olympics are also slated for Europe in the Russian city of Sochi, and the 2006 Winter Olympics were held in Turin, Italy. Bid head Coghen pointed out, however, that the IOC chooses "cities, not continents". It was Madrid's second consecutive failure, after losing out to London for the 2012 Olympics, and later in 2020, marking the city's third failure. The bid logo is a coloured hand print called "Corle" welcoming citizens to Madrid. An "m" is hidden in the palm standing for Madrid. It was selected via a public contest.

The Japanese Olympic Committee (JOC) chose Tokyo over Fukuoka in August 2006.^[62] Tokyo has recent experience with the success of the 2002 FIFA World Cup, which Japan co-hosted with South Korea. Japan also has past Olympic experience as the host of the 1964 Games in Tokyo, the 1972 Winter Games in Sapporo, and the 1998 Winter Games in Nagano. Tokyo touted "the most compact and efficient Olympic Games ever" with a dramatic setting on the shores of Tokyo Bay. Similar to other past winning cities, Tokyo pledged to refurbish a run-down industrial area, and to reclaim land from the bay. Despite massive campaigning in trains, parks and street, Tokyo's public support trailed behind the other lead cities. It fell to 56% in May 2009,^[63] from 62% in December 2007^[64] and 72% in March 2008,.^[65] While Tokyo continued its attempts to popularize the bid in high-profile venues^[66] and events, such as the Tokyo Marathon,^[67] the Beijing Games were held nearby in 2008.^[59] Specifically, the voting only one year after Beijing perhaps interfered with Tokyo's bid.^[68] Tokyo's logo was a musubi, a traditional knot which signifies times of blessing, in this case using the Olympic colors. Tokyo was the second city eliminated, leaving Rio de Janeiro in the run-off against Madrid to host the 2016 Summer Olympics. Tokyo was later chosen as host of the 2020 Summer Olympics in 2013.

On April 14, 2007, the United States Olympic Committee (USOC) chose Chicago to run in the 2016 Olympic bidding. Chicago was chosen to host the 1904 Summer Olympics but they would be held in St. Louis, to coincide with the 1904 World's Fair.^[69] The 1996 in Atlanta were the last summer Olympics to be hosted in North America. Chicago has an extensive public transit system, a wide range of venues, and a strong sports culture.^[70] The planned dramatic setting for Olympics on the shores of Lake Michigan, as well as the entirely urban experience were positive factors.^[59] Chicago is one of few cities in the United States to host professional men and women's hockey, baseball, basketball, soccer, and American football teams. Another benefit was the city's central location in the United States, since the Central Time Zone was well-suited to the North American television coverage for television networks and cable broadcasting, which in turn benefits NBC, the media company which pays the highest broadcasting rights to the IOC. Plans included a temporary Olympic Stadium in Washington Park on the city's South Side,^[71] a swimming venue on the West Side, and a number of events at McCormick Place convention center and the lakeshore as well as the Olympic Village just south of the Loop. However, soaring demolition costs to the hospital currently on the site would have required a new site for the village.^[72] 22 of the 27 Olympic venues would have been in four clusters within 15 km of the Olympic Village. Five new venues and eleven temporary venues would have been built for the games. The bid costs (US$49.3 million) were covered by the private sector.^[73] The bid was being promoted by Chicago-based media mogul Oprah Winfrey, Olympic champion Michael Phelps,^[74][75] NBA superstar and former Chicago Bulls player Michael Jordan, and by Chicago resident, U.S. President Barack Obama who attended the IOC vote in Copenhagen. However, local public support was smaller than other bidding cities^[76] and the city press ran articles against the bid. Chicago was reported by the media to be the strongest contender in terms of infrastructure, support, and money. However Chicago was ranked 3rd by an IOC evaluation report as to the technical aspect of their bid behind Tokyo and Madrid.^[77][78][59] Having received the fewest votes in the first round, Chicago was the first city eliminated from contention. This was seen as a major upset against the Chicago bid team.^[79] Eight years after Chicago losing the bid, Los Angeles was later won to host the 2028 Summer Olympics.^[80]

Azerbaijan's capital, Baku, announced its bid for the Olympics,^[81] with initial studies suggesting that the cost of hosting the 2016 Summer Olympics could be $20 billion. The capital of a petroleum rich nation with a booming economy, Baku had plenty of money to fund the games. Unfortunately, the city's infrastructure had deteriorated since the breakup of the Soviet Union. In addition, there are three frozen political conflicts in the South Caucasus region.^[82] A lesser factor considered by the IOC is the host nation's sport legacy. Azerbaijan has been an independent nation only a short time, so its Olympic history is also short, sending teams since only 1996 and claiming only three gold medals so far.^[59] The Azerbaijani Organizing Committee established its bid committee in November 2007, installing first vice premier Yagub Eyubov as head. Sports Minister Azad Ragimov was aided by the Caspian American Group to prepare the bid book with the assistance of the government.^[83] Baku's elimination was not unexpected, as one insider cited that practically no sports facilities meet global standards, the underdeveloped tourist sector, and regional conflicts. He cited 2020 or 2024 as times when Baku will have more serious arguments to win a bid.^[82] Baku's logo depicts petroglyph images from the Gobustan Rock Plateau, which features the remains of settlements and burials reflecting ancient human culture.^[84]

Doha submitted its bid to host the 2016 Summer Olympics^[85] after its hosting of the 2006 Asian Games, spending US$2.8 billion on infrastructure and venues.^[86] The Doha 2016 bid won much regional support, for example from the Olympic Council of Asia (OCA) president^[87] and the Gulf Cooperation Council. The Aspire Zone Sports City was to be the centerpiece of the bid, much as it served in the 2006 Asian Games. Qatar is in a growth period due to its petroleum reserves, and like Baku, is well situated to finance a large event. Doha is the only city in the Arab World other than Cairo to mount a serious bid, with pundits speculating the IOC may reward it by promoting it to the final shortlist. Although in a troubled area, Qatar is known as an open-minded country which is promoting acceptance and change and promoted a strong message of peace and acceptance for the region. In July and August, the average temperature in Doha can easily reach 45 °C (113 °F), thus they proposed mounting the Games in October. It is not without precedent (e.g. Mexico City and Sydney), but is technically outside the requirements. As Doha and Qatar in general (500,000 and 1,400,000 inhabitants, respectively) is among the smallest cities to bid to host the modern games, the Qataris would have to be innovative in bringing in spectators from neighboring countries to raise ticket sales. A side consideration is that like Azerbaijan, Qatar also has a short Olympic legacy,^[59] and has been criticised for its practice of giving "passports of convenience" to foreign athletes to pad their record.^[88] Only two new venues were to have been built, a velodrome and a baseball stadium, although a new Athletes' village was to be designed. Khalifa International Stadium currently seats 50,000, under the 60,000 to meet the IOC standards.^[89] Also, Qatar has plans to build the world's most advanced Paralympics stadium and the world's first underground stadium for matches during the 2011 AFC Asian Cup in Qatar. The Doha logo for the 2016 bid is the al dahma, the flower of the spring. The design uses motifs from traditional henna decorations and Doha is written in Arabic in the design.^[90]

On March 22, 2007, Prague confirmed its bid when the Prague Assembly voted 53-10-3 in support of launching an official bid. Regarded as one of the most beautiful and visited cities in Europe,^[91] Prague fulfills the cultural aspects that the IOC seeks in a candidate.^[59] With a strong sports history and excellent accommodations, Prague had potential to make a memorable host.^[59] However, Prague has few venues in place; the plans included building three sport centers – a velodrome for cyclists in Prague or Brno; a swimming stadium that would be constructed from the existing Prague-Sutka Aquapark; and the major Olympic complex to be built in Letnany. At the Aquapark, circular pools would be built to represent the Olympic rings. Other boating venues would be in Lipno, Racice, and Troja.^[92] Prague planned to use the Sazka Arena (now the O2 Arena) for gymnastics,^[92] and in some way the city planned to use or refurbish Strahov Stadium. Further details have stressed that perhaps only 30% of construction would leave a permanent legacy. After initial support from civic authorities such as mayor Pavel Bem, Prague's bid became a long-shot.^[93] Considering the lack of current stadia and other important Olympic sports infrastructure and the 2012 London hosting of the games, Prague was warming up for a later Olympic bid.^[59] Prague struggled with broader support in the Czech Republic; even president Václav Klaus publicly worried about budget estimates and white elephants.^[94] A public opinion poll in October 2007 mustered a quite low 50% support.^[95] Prague's bid logo features a branch from a laurel wreath, a traditional symbol of victory and celebration.