Childhood obesity is a major public health concern, linked to long-term health issues such as cardiovascular diseases and diabetes later in life. Brown adipose tissue, crucial for heat generation in newborns, diminishes with age, transitioning to white adipose tissue, however, if the transition happens earlier than at 5–7 years old due to overweight or obesity in infancy, obesity in adulthood is a threat. Adipocyte area was correlated with BMI z-scores, showing a positive relationship in 45 male patients aged 0.25–17 years. UCP1 immunocytochemical staining of isolated adipocytes revealed UCP1-positive cells across all samples. Next-generation sequencing analysis highlighted overrepresented transcripts associated with obesity in UCP1-negative samples, and a reduced expression of genes affiliated with the mitigation of adiposity and inflammation. PPARGC1A mRNA levels correlated significantly with UCP1 expression, indicating a link between mitochondrial content and thermogenic potential, and negative correlations were observed between adipocyte size and both UCP1 and PPARGC1A expression. Overall, the study suggests that UCP1 expression may serve as a marker for abnormal adipocyte development and offers potential diagnostic and therapeutic avenues for childhood obesity.