Aim: To analyse salivary cortisol levels in 12- and 24-month-olds from families with an anthroposophic lifestyle and comparisons (partly anthroposophic and non-anthroposophic). Methods: Salivary samples were collected at child ages of 12 (n = 178) and 24 (n = 149) months. Cortisol was analysed with radioimmunoassay technique. Results: Evening cortisol levels in children from anthroposophic families were lower than in comparisons at 12 months of age (geometric means: anthroposophic 1.7, partly anthroposophic 1.9, non-anthroposophic 3.6 nmol/L; p = 0.024) and at 24 months of age (1.1, 1.8 and 2.9 nmol/L, respectively; p = 0.002). At 24 months of age, similar differences were noted also for the afternoon levels (2.3, 3.3 and 3.9 nmol/L, respectively; p = 0.043). At age 12 months, the differences in the evening cortisol were statistically explained by a meat-free diet and at age 24 months by the anthroposophic lifestyle as such. The circadian variations were parallel in the three groups at age 12 and 24 months. No cortisol differences were observed between parents representing different lifestyles. Conclusions: An anthroposophic lifestyle is associated with low cortisol levels in the evening at age 12 and 24 months, at age 24 months also in the afternoon.