196 (C57BL/6J x BALB/cJ)F2 animals were used to map 14 QTLs associated with traits related to circadian behavior such as phase, period, and amplitude of activity. Genome scan was performed using 89 polymorphic markers at an average spacing of 20 cM. Parental inbred strain BALB/cJ exhibits shorter circadian period and unstable activity rhythms compared to parental inbred strain C57BL/6J which exhibits longer circadian period and stable activity rhythms. QTLs associated with free running period, Frp1, Frp2, and Frp3, mapped to 35.5 cM on mouse Chromosome 4, 72 cM on mouse Chromosome 5, and 22 cM on mouse Chromosome 12, respectively. C57BL/6J-derived alleles appear to confer shorter running periods at Frp1 (additive inheritance) and Frp2 (dominant inheritance). Frp3 was detected via pairwise analyses to detect interacting loci and displays moderate interaction with Frp2 (P = 0.0012). Frp1 and Frp2 were not shown to interact. QTLs associated with angle of entrainment, Angle1, Angle2, Angle3, Angle4, and Angle5, mapped to 1 cM and 50 cM on mouse Chromosome 12, 20 cM on mouse Chromosome 18, 37 cM on mouse Chromosome 7, and 67 cM on mouse Chromosome 8, respectively. Pairwise analyses revealed significant interactions between Angle2 and Angle5, while Angle1 and Angle 3 may have weak interactions. QTLs associated with amplitude of circadian rhythm, Amp1 and Amp2, mapped to 42.5 CM on mouse Chromosome 4 and 81.6 cM on mouse Chromosome 1, respectively. C57BL/6J-derived alleles appear to exhert a semidominant effectat Amp1, and Amp2 was detected via pairwise analyses with Amp1. Homozygosity for C57BL/6J-derived alleles at Amp1 in combination with homozygosity for BALB/cJ-derived alleles at Amp2 appears to increase amplitude of activity in (C57BL/6J x BALB/cJ)F2 animals. QTLs associated with activity levels, Actvty1 and Actvty2, map to 71.45 cM on mouse Chromosome 16 and 3.7 cM on mouse Chromosome X, respectively. Actvty1 and Actvty2 show significant interaction in female animals. QTLs associated with dissociation of activity rhythms, Disso1 and Disso2, mapped to 29 cM on mouse Chromosome 12 and 43.7 cM on mouse Chromosome 15, respectively. Disso1 and Disso2 show significant interaction: animals homozygous for C57BL/6J-derived alleles at Disso1 and homozygous for BALB/cJ-derived alleles at Disso2 show high values of dissociation of activity rhythms.