Background: This study aims at identifying predictors of the treatment decision of German physicians with regard to a non-nucleoside reverse transcriptase inhibitor (NNRTI) or a ritonavir-boosted protease inhibitor (PI/r) -based initial treatment regimen. Methods: The study is based on a sub analysis of a nation-wide multi-centre, non-interventional, prospective cohort study. 133 patients were identified, who received antiretroviral first-line therapy. By means of a logistic regression, factors that determine the treatment strategy for treatment-naïve patients were analysed. Results: Compared to patients receiving a NNRTI-based initial regimen, patients treated with PI/r are slightly younger, less educated, in a later stage of HIV and have more concomitant diseases. Regression analysis revealed that being in a later stage of HIV (CDC-C) is significantly associated with a PI/r-based treatment decision. Conclusions: Our analysis is the first study in Germany investigating sociodemographic and disease-specific parameters associated with a NNRTI- or a PI/r-based initial treatment decision. The results confirm that the treatment decision for a PI/r strategy is associated with disease severity.