Influenza-infected C57BL/6J mice spend increased amounts of time in slow-wave sleep (SWS) during the dark phase of the circadian cycle compared to healthy mice. In contrast, infected BALB/cByJ mice show a normal or reduced time in SWS, particularly during the light phase. To identify genetic loci with linkage to these traits, we measured sleep in 13 CXB recombinant inbred (RI) strains derived from a cross between C57BL/6ByJ and BALB/cByJ mice. The probability density distribution of sleep patterns of influenza-infected CXB RI mice showed modes that correspond roughly with the parental modes during the dark phase of the circadian cycle and are intermediate or C57BL/6-like during the light phase. These patterns are consistent with the presence of a low number of major effect quantitative trait loci (QTLs). Chromosomal regions with provisional association to strain variation in influenza-induced SWS patterns were identified. In particular, a 10- to 12-cM interval on Chr 6 between D6Mit74 and D6Mit188 contains a QTL (LRS = 16.6 at 1 cM proximal to D6Mit316; genomewide p < .05) that influences the SWS response to influenza infection during the light phase. We have provisionally named this QTL Srilp1 (sleep response to influenza, light phase 1). Candidate genes for mediation of this phenotype include Ghrhr (growth hormone releasing hormone receptor), Crhr2 (corticotropin releasing hormone receptor 2), and Cd8a (an epitope on cytotoxic T lymphocytes). Several other intervals achieved suggestive probability scores that are sufficient to warrant further analysis either with additional RI strains or with F2 panels. The analysis also suggests that dark phase and light phase responses are regulated by different genetic factors.