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Future strategies aiming to achieve HIV-1 remission are likely to target individuals with small reservoir size.We retrospectively investigated factors associated with HIV-1 DNA levels in European, perinatally HIV-infected children starting antiretroviral therapy (ART) <6 months of age.Total HIV-1 DNA was measured from 51 long-term suppressed children aged 6.3 years (median) after initial viral suppression. Factors associated with log10 total HIV-1 DNA were analyzed using linear regression.At ART initiation, children were aged median [IQR] 2.3 [1.2–4.1] months, CD4% 37 [24–45] %, CD8% 28 [18–36] %, log10 plasma viral load (VL) 5.4 [4.4–5.9] copies per milliliter. Time to viral suppression was 7.98 [4.6–19.3] months. After suppression, 13 (25%) children had suboptimal response [≥2 consecutive VL 50–400 followed by VL <50] and/or experienced periods of virological failure [≥2 consecutive VL ≥400 followed by VL <50]. Median total HIV-1 DNA was 43  copies/106 PBMC. Younger age at therapy initiation was associated with lower total HIV-1 DNA (adjusted coefficient [AC] 0.12 per month older, P = 0.0091), with a month increase in age at ART start being associated with a 13% increase in HIV DNA. Similarly, a higher proportion of time spent virally suppressed (AC 0.10 per 10% higher, P = 0.0022) and the absence of viral failure/suboptimal response (AC 0.34 for those with fail/suboptimal response, P = 0.0483) were associated with lower total HIV-1 DNA.Early ART initiation and a higher proportion of time suppressed are linked with lower total HIV-1 DNA. Early ART start and improving adherence in perinatally HIV-1–infected children minimize the size of viral reservoir.