Aim of this study was the examination of fetal heart rate variability and complexity measures during pregnancy using fetal magnetocardiography. We registered 80 fetal magnetocardiograms in 19 healthy fetuses between the 16th and 41st week of gestation. On the basis of beat to beat intervals, mean RR interval (mRR), its standard deviation (SD), root mean square of successive differences (RMSSD), as well as complexity variables such as dimension (ApD1), entropy (ApEn), Lyapunov exponent (ApML) and trajectory divergence rate (p) were calculated for each recording. Dependency of these variables on gestational age was evaluated with correlation analysis. All variables changed consistently over time. RMSSD showed the strongest dependency on gestational age, followed closely by ApEn, SD and p. ApD1 and mRR showed only weak dependency. We conclude that magnetocardiography is well suited to register fetal cardiac activity with sufficient accuracy to permit detailed analysis of various heart rate variables during the second and third trimester of pregnancy. The observed increases in heart rate variability and complexity of fetuses most likely reflect differing but overlapping aspects of fetal development. They may be linked to the maturation of the autonomic nervous system and could aid in the timely identification of pathological conditions.