Improved cold tolerance during the juvenile phase is a major breeding goal to develop new sorghum cultivars suitable as an alternative energy crop in temperate regions. The objectives of this study were to identify marker-trait associations for cold tolerance in a sorghum diversity panel fingerprinted with 2620 single nucleotide polymorphism (SNP) markers and to detect quantitative trait loci (QTL) in two F2:3 populations. Traits of interest were dry matter growth rate (DMGR), leaf appearance rate (LAR), chlorophyll content (SPAD) and chlorophyll fluorescence (Fv′/Fm′ and ФPSII) in relation to temperature. The association panel comprised 194 genotypes, while the F2:3 populations consisted of 80 and 92 genotypes. All populations were tested under controlled conditions in a minimum of four temperature regimes ranging from 9.4°C to 20.8°C. QTL were identified for means across environments and regression parameters describing temperature effects. Several marker-trait associations for mean (m) DMGR, base temperature (Tb) of SPAD and ФPSII and temperature effect on LAR were validated by QTL detected in population 1 or 2. Promising QTL regions were found on chromosomes SBI-01, SBI-02, SBI-03, SBI-04, SBI-06 and SBI-09, among them genomic regions where candidate genes involved in the C-repeat binding pathway or encoding cold-shock proteins are located.