Genome-wide association studies (GWAS) have identified genetic loci associated with cutaneous squamous cell carcinoma (cSCC) risk, but single nucleotide polymorphisms (SNP) associations with cSCC invasiveness have not been investigated. We examined associations between cSCC invasiveness and 23 reported SNPs among 67,833 non-Hispanic white subjects. Additionally, we performed a genome-wide scan and identified one SNP with significantly different frequencies in 5,724 subjects with at least one invasive tumor and 1,943 subjects with in-situ tumors only. We then compared genotype frequencies among the invasive and in-situ groups with those of 60,166 control subjects. The genome-wide scan identified that the T allele in SNP rs41269979 in the class II human leukocyte antigen region was more frequent in the invasive than the in-situ group (P = 4.93x10(-8)). SNPs in five of the 23 previously-associated loci showed OR heterogeneity between the in-situ and invasive groups: rs447510 in HLA-DQA1 (Phet = 2.93x10(-3)); rs12203592 in IRF4 (Phet = 3.94x10(-4)); rs1805007 in MC1R (Phet = 7.71x10(-3)) and two SNPs in DEF8 (rs4268748, Phet = 1.09x10(-4) and rs8063761, Phet = 1.40x10(-4)). These findings may provide new insight into the genetic basis of cSCC invasiveness and may help identify individuals at higher risk for developing clinically aggressive cSCC.