The evidence of weakening of T cells emigration from thymus to peripheral immune system in children with thymomegaly is presented. It means the thymopoiesis is reduced in children with thymomegaly. The thymic emigration was investigated by two methods: real time PCR (the TREC level was measured) and flow cytometry (the number of CD3+CD4+CD45RA+CD31+ cells was measured). It was shown that the number of TREC copies per 1000 lymphocytes is significantly decreased in children with thymomegaly till 10 years. The TREC level in children with thymomegaly till 2 years approximately fits to the normal level of 8 years old children at which functional thymic activity is reduced in comparison with smaller children. In parallel with TREC level decrease with age the percentage and absolute content of CD3+CD4+CD45RA+CD31+ cells in blood is also decreased. However the TREC reduce is more intensive than CD3+CD4+CD45RA+CD31+ cells number decrease. The investigation of CD3+CD4+CD45RA+CD31+ cells number in blood of 2-10 years children with thymomegaly and without it showed that the number of cells of this subpopulation in thymomegaly is not changed.