Aim. To develop a methodology for individual, group, regional and population health estimation. Methods. Offered methodology includes physical health assessment and assessment of morphologic and functional condition of organ systems in a healthy human. Physical health assessment was performed in 808 young males aged 17-21 years in the city of Krasnoyarsk. Anthropometry, body mass index calculation, Tanner maturation index, ageing speed coefficient calculation by B.B. Gorelkin and A.G. Pinhasov, bioelectrical impedance analysis and statistical analysis were performed. Results. Youth males had a height of 176.87±0.26 sm, body weight of 69.23±0.45 kg. According to calculated body mass index, healthy weight was found in 71.41% males, 12.75% were overweight, 3.96% were obese, 11.88% were underweight. Shoulders and pelvis diameters were assessed as 37.01±0,11 and 27.72±0.09 sm respectively. Tanner maturation index calculation has shown that 54.83±1.20% males were andromorphous, the others had different types of gender inversions: 18.69±0.94% were hynecomorphous, 26.49±1.07% were mesomorphous. Ageing speed coefficient calculation has revealed the discrepancy of calendar and biologic age (the latter was higher) in all hynecomorphous young males, meaning that hynecomorphism can be estimated as a predictor of early ageing and can be used in complex health assessment. The core of the offered methodology for population health estimation is the health assessment on all stages of ontogenesis, including all levels from organism to molecular, that would allow to develop the standards for health assessment and assessment of morphologic and functional condition of organ systems. Conclusion. The listed methods would allow to estimate organism’s morphologic and functional condition, and revealed physical development abnormalities would allow to correct them timely before the clinical onset of any diseases.