Purpose. Contamination of contact lens cases has been associated with the production of adverse responses in the eye during contact lens wear. This study aimed to evaluate the contamination rate and types of microbes contaminating cases during use of contact lens disinfecting solutions and silicone hydrogel lenses. Methods. Two hundred thirty-two participants were allocated to one or more groups. The participants wore one or more of three silicone hydrogel lenses and used one or more of four contact lens disinfecting solutions. Cases were collected after use for 1 month and sent for routine microbial testing. The rate of contamination of cases and the types of microbes contaminating cases were evaluated. Results. Between 76 and 92% of all cases were contaminated. Use of different contact lenses did not affect contamination rate or the types of microbes isolated from cases. Use of AQuify (PHMB as disinfectant) was associated with the highest contamination rate (92%; p = 0.015) of cases for any microbe. Level and type of contamination with use of ClearCare (H 2O2) was similar to use of PHMB (polyhexamethylene biguanide)- or Polyquat/Aldox-containing solutions. There was no difference in contamination rate of cases by fungi or Gram-positive bacteria, but for Gram-negative bacteria, use of Opti-Free Express (Polyquat and Aldox as disinfectants) resulted in a lower contamination rate (7% vs. 29 to 45%; p < 0.001). The average number of microbes contaminating a case was significantly less for Opti-Free Express (223 ± 1357 cfu/case) compared with Opti-Free RepleniSH (Polyquat and Aldox as disinfectants; 63,244 ± 140,630 cfu/case; p < 0.001), driven mostly by differences in numbers of Gram-negative bacteria, particularly contamination by Delftia acidovorans in cases exposed to Opti-Free RepleniSH. Conclusions. Different disinfecting solutions used during storage in cases result in different levels of contamination and contamination by different types of microbes. These differences are not simply because of the types of disinfectants used, suggesting that other excipients in, or formulation of, the solution affect contact lens storage case contamination.