High attrition and irregular testing for human immunodeficiency virus (HIV) in cohort studies for high-risk populations can bias incidence estimates. We compare incidence trends for high-risk women attending a dedicated HIV prevention and treatment clinic, using common methods for assigning when seroconversion occurs and whether seroconversion occurs among those with attrition. Between April 2008 and May 2009, women were enrolled into cohort 1 and from January 2013 into cohort 2, then scheduled for follow-up once every 3 months. Incidence trends based on assuming a midpoint in the seroconversion interval were compared with those of assigning a random-point. We also compared estimates based on the random-point with and without multiple imputation (MI) of serostatuses for participants with attrition. By May 2017, 3084 HIV-negative women had been enrolled with 18,364 clinic visits. Before attrition, 27.6% (6990 of 25,354) were missed visits. By August 2017, 65.8% (426 of 647) of those enrolled in cohort 1 and 49.0% (1194 of 2437) in cohort 2 were defined with attrition. Among women with 1 or more follow-up visit, 93 of 605 in cohort 1 and 77 of 1601 in cohort 2 seroconverted. Periods with longer seroconversion intervals appeared to have noticeable differences in incidences when comparing the midpoint and random-point values. The MI for attrition is likely to have overestimated incidence after escalated attrition of participants. Based on random-point without MI for attrition, incidence at end of observation was 3.8/100 person-years in cohort 1 and 1.8/100 in cohort 2. The random-point approach attenuated variation in incidence observed using midpoint. The high incidence after years of ongoing prevention efforts in this vulnerable population should be investigated to further reduce incidence.