Abstract Background Most sequencing studies in Parkinson’s disease (PD) have focused on either a particular gene, primarily in familial and early onset PD samples, or on screening single variants in sporadic PD cases. To date, there is no systematic study that sequences the most common PD causing genes with Mendelian inheritance [ α-synuclein ( SNCA ), leucine-rich repeat kinase 2 ( LRRK2) , PARKIN , PTEN-induced putative kinase 1 ( PINK1 ) and DJ-1 (Daisuke-Junko-1) ] and susceptibility genes [ glucocerebrosidase beta acid ( GBA ) and microtubule-associated protein tau ( MAPT )] identified through genome-wide association studies (GWAS) in a European-American case-control sample (n=815). Results Disease-causing variants in the SNCA, LRRK2 and PARK2 genes were found in 2 % of PD patients. The LRRK2 , p.G2019S mutation was found in 0.6 % of sporadic PD and 4.8 % of familial PD cases. Gene-based analysis suggests that additional variants in the LRRK2 gene also contribute to PD risk. The SNCA duplication was found in 0.8 % of familial PD patients. Novel variants were found in 0.8 % of PD cases and 0.6 % of controls. Heterozygous Gaucher disease-causing mutations in the GBA gene were found in 7.1 % of PD patients. Here, we established that the GBA variant (p.T408M) is associated with PD risk and age at onset. Additionally, gene-based and single-variant analyses demostrated that GBA gene variants (p.L483P, p.R83C, p.N409S, p.H294Q and p.E365K) increase PD risk. Conclusions Our data suggest that the impact of additional untested coding variants in the GBA and LRRK2 genes is higher than previously estimated. Our data also provide compelling evidence of the existence of additional untested variants in the primary Mendelian and PD GWAS genes that contribute to the genetic etiology of sporadic PD.