Objectives: Data on drug-resistant mutations (DRMs) in HIV-1-infected therapy-naïve children are scarce. The aim of this study was to determine the HIV-1 subtype distribution and the prevalence of DRMs in therapy-naïve HIV-1-infected children who received routine care at the University Hospital Düsseldorf, Düsseldorf, Germany. Methods: Records of all HIV-1-infected children who received routine care between January 2005 and December 2015 were analyzed retrospectively. The collected data included demographics, clinical characteristics, CD4 cell count, viral load, HIV-1 subtype, and resistance genotype at baseline. Results: 83 HIV-1-infected children received routine care during the observation period. HIV-1 subtypes were available in 61/83 patients (73.5%) and baseline HIV-1 resistance in 24 (29%). The prevalence of major DRMs was 29% (21% nucleoside reverse-transcriptase inhibitors [NRTIs], 12.5% non-NRTIs, and 4% protease inhibitors). Minor mutations in the protease gene were common (58%). Non-B subtypes were predominant (77%). Conclusions: We report a predominance of non-subtype-B infections and a higher prevalence of DRMs compared to other pediatric cohorts from resource-rich settings. The difference in HIV-1 subtype distribution is due to the fact that a relevant proportion of pediatric patients in Germany are immigrants from high-prevalence settings in sub-Saharan Africa where non-B subtypes predominate.