Background : HIV infection is endemic in Nigeria and is an important cause of infant mortality and morbidity. This study was undertaken to determine the sero-epidemiology of HIV among abandoned babies in Port Harcourt, Nigeria. Methods : One hundred and forty (n = 140) consecutively recruited abandoned babies mean age 11.5 ± 24.1 weeks made up to 79 males and 61 females, referred to the HIV screening unit from motherless babies home in Port Harcourt for pre-adoption HIV screening within a five years period (1999– 2003) were screened for HIV using the WHO approved immunocomb HIV I& II kits (Organics, Israel)– an enzyme linked immunosorbent assay for the quantitative and differential diagnosis of HIV in serum or plasma. Initially reactive samples were continued using Genscreen HIV 1& 2 (p24) antigen test (Bro Rad, France). Results :HIV was detected in 19(13.6%) of babies tested. Sero-prevalence was highest in babies 9– 16 weeks (25.0%). Males accounted for the highest infection burden (57.9%) compared to (42.1%) for females. Data indicated that the prevalence of HIV declined from 12.5% in 1999 to 8.3% in 2000 and increased subsequently to 20% in 2001 but declined steadily to 16.1% in 2002 and 14.3% in 2003. HIV-1 accounted for the predominant viral subtype among babies sero-positive for HIV (89.5%). Chi square analysis indicates that symptom at abandonment was an independent risk factor for HIV infection among abandoned babies (χ2 = 40.97; p = 0.0001). Conclusions : This study demonstrates a high prevalence of HIV among abandoned babies in Port Harcourt. This calls for an urgent need for government, non governmental organization and faith-based organization to critically examine the issue of child abandonment and HIV infection by initiating care and support programme aimed at providing knowledge and information which emphasizes a combination of behavioural and social changes and providing a youth-friendly health services to control the HIV scourge.