Acquired Immune Deficiency Syndrome (AIDS) is one of the leading health problems in Papua and antiretroviral (ARV) therapy increases cluster of differentiation 4 (CD4(+)). We examined whether the CD4(+) counts correlated with factors affecting adherence of ARV therapy in Papua. A cross-sectional study was conducted from June to September 2017 at VCT RSUD Dok II Jayapura. We assessed 85 respondents receiving ARV therapy, or 12-24 months, who had fiitfilled inclusion criteria agreed to sign the informed consent. Information of CD4(+) and factors affecting adherence were obtained from blood samples analysis and questionnaires. Data were analyzed using Fisher exact test and Odds Ratio at p<0,05. The result showed that the high percentages of respondents' characteristics include female, aged 15-30 years, employed, had formal education, indigenous Papuan, good treatment knowlegde, never switch ARV had ARV side effects, had health insurance, never stigmatized, always got adherence counseling, easy access to health services, had family support, no community support. Most of the respondents were adherent to taking ARVs and had an increase in CD4(+) cell counts. Women, working status, and stigma had a greater risk for immunodeficiency. Evaluation was required for respondents whose good adherence but did not experienced an increase in CD4(+) cell counts.