BACKGROUND: High attrition and irregular testing for 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. METHODS: Between April 2008-May 2009 women were enrolled into cohort-1 and from January 2013 into cohort-2, then scheduled for follow-up once every three months. Incidence trends based on assuming a mid-point in the seroconversion interval were compared to those of assigning a random-point. We also compared estimates based on the random-point with and without multiple imputation (MI) of sero-status for participants with attrition. RESULTS: By May 2017, 3084 HIV-negative women had been enrolled with 18,364 clinic visits. Before attrition, 27.6% (6,990/25,354) were missed visits. By August 2017, 65.8% (426/647) of those enrolled in cohort-1 and 49.0% (1194/2437) in cohort-2 were defined with attrition. Among women with ≥1 follow-up visit, 93/605 in cohort-1 and 77/1601 in cohort-2 seroconverted. Periods with longer seroconversion intervals appeared to have noticeable differences in incidences when comparing the mid-point and random-point values. MI for attrition is likely to have overestimated incidence following 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. CONCLUSION: The random-point approach attenuated variation in incidence observed using mid-point. The high incidence after years of ongoing prevention efforts in this vulnerable population should be investigated to further reduce incidence.