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Late presentation to healthcare by HIV infected patients’ is common in India despite access to free combination antiretroviral therapy (cART). We assessed risk factors for late presentation among patients with a recent HIV diagnosis in an academic university–based antiretroviral treatment center. This retrospective study included 474 recently diagnosed HIV-infected patients registered for cART between 2012 and 2013. Subjects with CD4(+) T-lymphocyte (CD4) count ≤ 350 cells/μL or with an AIDS defining event were defined as late presenters (LP) and patients with CD4 count ≤ 200 cells/μL or with an AIDS defining event were defined as LP with advanced HIV disease (LPAD). Multivariable logistic regression analysis was used to investigate factors associated with late presentation. Of the 474 patients, 356 (75.1%) were LP. Of these, 299 (83.99%) were LPAD and 57 (16.01%) LP were AIDS-free. Median CD4 count among LP was 134 cells/μL (interquartile range 72.25–219). Mean age of LP was 42.50 ± 8.88 years; 256 (71.9%) were males. Increasing age (> 51 years; Adjusted odds ratio [aOR] 4.19; P = 0.014) and rural residence (aOR 3.19; P = < 0.001) were independently associated with late presentation. HIV-positive housewives (aOR 0.34; P = 0.027), HIV-positive individuals with negative partners (aOR 0.48; P = 0.006), and partners with unknown HIV status (aOR 0.43; P = 0.007) were less likely to present late compared with positive partners of people living with HIV/AIDS (PLWHA). Most patients were LP despite free access to cART. Rural population and older PLWHA should be targeted while implementing HIV care. There is a need to strengthen the HIV care cascade by linking PLWHA to cART immediately after diagnosis.