Despite the recommendation for early diagnosis and rapid initiation of HIV treatment, more than half of patients are in an advanced stage of HIV disease in Iran. This study aimed to investigate the factors related to baseline CD4 cell count and advanced HIV disease (AHD) in Southern Iran. The study comprised all adults between 15 and 87 years of age who were newly diagnosed with HIV in Southern Iran. Linear and logistic regressions were used to identify baseline CD4 cell count predictors and AHD, respectively. A total of 820 (53.9%) HIV-infected individuals over 15 years of age were at the AHD stage. Based on the results of the multiple logistic regression, older age at diagnosis (OR≥40/<30 = 2.68, 95% CI = 1.38–5.19), gender (ORfemale/male = 0.62, 95% CI = 0.44–0.85), HIV/TB coinfection (ORyes/no = 1.98, 95% CI = 1.29–3.02), HIV/HBV coinfection (ORyes/no = 1.58, 95% CI = 1.07–2.38), and hemoglobin (OR = 0.89, 95% CI = 0.85–0.92) were directly associated with AHD in HIV/AIDS patients. As suggested by a linear regression model, factors including gender (B Female = 44.12, 95% CI:17.86, 70.38), older age (B ≥ 40 = −111.99, 95% CI:−174.70, −49.27), higher education level (B = 35.65, 95% CI:5.34, 65.97), WHO clinical stage (BIV = −254.53, 95% CI−298.82, −210.24), and hemoglobin (B = 5.23, 95% CI:0.25, 10.20) were significantly associated with CD4 count.The prevalence of AHD in patients was high in Iran. Our results suggested that several demographic and clinical factors are significantly associated with the baseline CD4 cell count and AHD. Targeted HIV testing, implementation of screening programs for early detection, and access to care services to assure early ART are recommended to improve the clinical status and quality of life of the patients.