Introduction: Determining genetic contribution to development of complicated community-acquired pneumonia in children may help understand underlying pathogenesis. We aimed to investigate the association between two vitamin D receptor (VDR) gene polymorphisms, FokI and TaqI, and susceptibility to complicated pneumonia in Egyptian children compared to uncomplicated pneumonia, also associations with 25 hydroxy-vitamin D serum level were studied. Methods: This was a case-control study that included 320 participants divided into 2 groups: patients and controls. The patients’ group included 100 children hospitalized with complicated pneumonia and 100 with uncomplicated pneumonia. 120 age and sex-matched apparently healthy children served as controls. The VDR FokI and TaqI polymorphisms were genotyped using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique. 25 hydroxy-vitamin D level was estimated in serum using ELISA. Results: Regarding FokI, Homogenous FF genotype was more common in complicated (52%) and uncomplicated pneumonia (28%) than controls (10%) (OR=65; 95%CI (5.13-822.63), p<0.001) and (OR=4.3; 95%CI (0.7-27.16), p=0.003), respectively. Children carrying F allele possessed 3 higher odds for complicated than uncomplicated pneumonia (OR=3.08; 95%CI (1.33-7.14), p<0.001). Heterogenous Ff genotype increased susceptibility to complicated pneumonia (OR=13.7; 95%CI (4.6-40.1), p<0.001), not uncomplicated pneumonia (OR=1.56; 95%CI (0.86-2.85), p=0.145). Among complicated pneumonia, vitamin D level was lower in FF (6.92±2.6ng/ml) than Ff (9.55±3.2 ng/ml) and ff genotype carriers (13.13±3.6ng/ml) (p<0.001). There was no significant difference between patients and controls as regards TaqI genotypes and alleles. Conclusion: In association with vitamin D deficiency, VDR gene FokI polymorphism, not TaqI, is a genetic risk factor for complicated pneumonia in Egyptian children.