Abstract. Our study is based on an extensive photometric monitoring program in the young (2-4 Myr) open cluster NGC 2264 by Lamm et al. (2004a). This program resulted in a sample of 405 periodic variables which are most likely pre-main sequence (PMS) members of the cluster. The periodic variability of these stars results from the rotational modulation of the light by stellar spots. In this paper we investigate the rotation period evolution of young stars. This is done by comparing the period distribution of the older NGC 2264 with that of the younger Orion Nebular Cluster (ONC, age: ∼1 Myr) which is known from the literature. The age ratio between the two clusters was estimated on the basis of PMS models to be about 2 +0.75 −0.5 . We find that the period distribution of NGC 2264 is similar in form to the ONC but shifted to shorter periods. In both clusters the period distribution depends strongly on the mass and it is bimodal for higher mass stars with M > ∼ 0.25 M while it is unimodal for lower mass stars with M < ∼ 0.25 M . In addition the lower mass stars rotate much faster on average than the higher mass stars. Quantitative comparison between the period distributions of both clusters suggests that a large fraction (about 80%) of stars have spun up from the age of the ONC to the age of NGC 2264. Based on this estimate and the estimated age ratio between the two clusters we find that the average spin up by a factor of 1.5−1.8 from the age of the ONC to the age of NGC 2264 is consistent with a decreasing stellar radius and conservation of angular momentum, for most stars. However, within NGC 2264 we did not find any significant spin up from the younger to older stars in the cluster. We also found indications for some ongoing disk-locking in NGC 2264, in particular for the higher mass stars. Our analysis of the period distribution suggests that about 30% of the higher mass stars in NGC 2264 could be magnetically locked into co-rotation with their inner disk. In the case of the lower mass stars, disk-locking seems to be less important for the rotational evolution of the stars. This interpretation is supported by the analysis of the stars' Hα emission. This analysis indicates that the locking period of the higher mass stars is about P = 8 days. For the lower mass stars this analysis indicates a locking period of about 2-3 days. We argue that the latter stars are probably not "completely" locked to their disk and propose an evolution scenario for these stars which we call "moderate angular momentum loss". In this scenario angular momentum is continuously removed from the stars but at a rate too low to lock the stars with a constant rotation period. We have done a detailed comparison with the recently published rotational period study of NGC 2264 of Makidon et al. (2004). Even though their obtained period distribution of their quality 1 data on NGC 2264 is indistinguishable within the statistical errors from ours, we come to quite different conclusions about the interpretation. One major reason for these discrepanci...