In 2009-2010, females who reported having vaginal, anal or oral sex in exchange for money in the previous year, ≥16 years, and living in either Chisinau (n = 299) or Balti (n = 359), Moldova, were recruited into a respondent driven sampling survey. One fifth reported ever injecting drugs and over 30 % ever had sexual intercourse with men who inject drugs. In both cities, condom use with permanent and casual partners was much lower than condom use with commercial partners. In Chisinau, 6.9 % and in Balti, 24.7 % tested positive for HIV; 18 and 23.7 % had antibodies to hepatitis C; 9.1 and 8.9 % had antibodies to HBV; and, 8.4 and 6.1 % tested positive for syphilis. HIV seropositive FSW in either city were more likely to have ever injected drugs and to be infected with HCV. Limited government initiative and drastic reductions in international funding will likely impact urgently needed HIV prevention and harm reduction services targeting FSW in Moldova.