Despite the known benefits of early treatment initiation for individual morbidity and mortality, as well as for reducing the risk of transmission, late presentation (LP) to HIV/AIDS services remains a major concern in many countries. There is little information on LP from middle- and low-income countries and studies that do evaluate LP commonly disaggregate data by sex. It is rare, however, for researchers to further disaggregate the data by pregnancy status so it remains unclear if pregnancy status modifies the effects associated with sex. The study was conducted at the only State Reference Center for HIV/AIDS in Salvador, Brazil's third largest city. LP was defined as a patient accessing services with a CD4 < 350 cells/mm3. Data were abstracted from the electronic medical records of 1421 patients presenting between 2007 and 2009. CD4 counts and viral load (VL) information was validated with data from the National CD4/VL Database. Descriptive and bivariate statistics were conducted to inform the multivariate analysis. Adjusted prevalence ratios (APR) were estimated using generalized linear models due to the high frequency of the outcome. Half of the sample (52.5%; n = 621) was classified as LP. Compared to the prevalence among pregnant women (21.1%), the prevalence of LP was more than twice as high among non-pregnant women (56.0%) and among men (55.4%). The multivariate analysis demonstrated no statistical difference between men and nonpregnant women (APR 1.04; 95%CI 0.92-1.19), but the APR of LP for nonpregnant women was 53% less than men (APR 0.47; 95%CI 0.33-0.68). These results highlight the importance of analyzing data disaggregated not only by sex but also by pregnancy status to accurately identify the risk factors associated with LP so that programs and policies can effectively and efficiently address LP in Brazil and beyond.