To evaluate the nutritional, clinical and immunological status of children at HIV diagnosis in the continental region of Equatorial Guinea. Children <18years diagnosed with HIV between 2009 and 2017 were included. Clinical, immunological and nutritional data were collected. Weight-for-height, weight-for-age and height-for-age Z-scores were calculated using WHO Child Growth Standards. The population was assessed in two equal periods (2009-2013 and 2014-2017) from the time of diagnosis. A total of 213 children were diagnosed with HIV (49.3% males), median age 3.8years (IQR: 1.5-8.2). A total of 121 cases (56.8%) were at WHO clinical stage III, and 53 (24.9%) were at WHO clinical stage IV. CDC immunological stage II was diagnosed in 51/130 (39.2%) and CDC stage III in 44/130 (33.8%). About 56.2% of children were underweight (weight-for-age <-2 SD); 20.1% moderately and 36.1% severely so. About 27.6% of children were wasted (weight-for-height <-2 SD); 11.9% moderately and 15.7% severely so. About 56.3% of children were stunted (height-for-age <-2 SD); 20.7% moderately and 35.6% severely so. The prevalence of wasting was higher in children ≤5years than in children >5years (36.4% vs. 19.1%, P=0.026). In the second period, the prevalence of moderate-severe immunodeficiency decreased (87.2% to 67.0%, P=0.018), without significant differences in the other nutritional or clinical data. Severe underweight was a risk factor for moderate-severe immunodeficiency (aOR: 4 [95% CI: 1.4-11.4], P=0.010). We highlight a high proportion of malnutrition at the time of HIV diagnosis in Guinea´s paediatric population. Early diagnosis of HIV infection is a priority, achievable by training Guinea´s physicians to suspect HIV early, introducing HIV molecular diagnostic techniques and ensuring intensive nutritional treatment.