Social marginalisation and other challenges facing HIV-positive pregnant women in Ukraine may put them at increased risk of relinquishing their infants to the state. We described rates of infant abandonment (exclusive non-parental care to most recent follow-up, censored at two years of age) and investigated associated factors using logistic regression models, in 4759 mother–infant pairs enrolled across six Ukrainian sites in the European Collaborative Study from 2000 to May 2009. Median maternal age was 26.0 years, 81.8% were married or cohabiting and 60.6% were nulliparous at enrolment. An injecting drug use (IDU) history was reported by 18.4%, 80.2% took antiretroviral therapy (ART) antenatally and most deliveries were vaginal. A small but significant proportion of infants had been cared for exclusively in institutions by their second birthday (2.1% overall), decreasing from 3.8% (15/393) in 2000–2002 to 1.6% (49/3136) in 2006–2009 (p<0.01), concurrent with prevention of mother-to-child transmission scale-up. A further 1% of infants spent some time in non-parental care. Antenatal ART was associated with an 88% reduced abandonment risk (adjusted odds ratio (AOR) 0.12), versus receipt of single dose nevirapine only, and this was reflected in HIV infection prevalence in the two groups (17.1% of abandoned infants versus 6.6% in parental care). Mothers without a cohabiting partner or husband were more likely to abandon (AOR 4.08), as were active IDUs (AOR 3.27) and those with =1 previous children (AOR 1.89 for second-born and AOR 2.56 for subsequent births). Women delivering by elective caesarean section were less likely to abandon (AOR 0.37 versus vaginal), as were those leaving full-time education later (AOR 0.61 for 17–18 years versus =16 years and AOR 0.23 for =19 years versus =16 years). Interventions to extend family planning and IDU harm reduction services along with non-stigmatising antenatal care to marginalised women are needed, and may reduce abandonment.