Accurate determination of resistance is important to ensure appropriate antimicrobial therapy in Stenotrophomonas maltophilia infections. This study was undertaken to evaluate the susceptibility results obtained by disc diffusion, E-test, Phoenix system, and reference agar dilution method and also to evaluate the in vitro activity of various antimicrobial combinations against multidrug-resistant S. maltophilia. Susceptibilities to several antimicrobial agents were determined by agar dilution, disc diffusion, and E-test according to the US Clinical Laboratory and Standards Institute (CLSI) guidelines. Results were also evaluated in the in Phoenix system for available agents. Twelve different antibiotic combinations were tested for synergy by the E-test method. Most synergic combinations were confirmed by microdilution checkerboard assay. Tigecycline, trimethoprim/sulfamethoxazole (TMP-SMX) and doxycycline were the most effective drugs against S. maltophilia. Poorest agreement was determined by disc diffusion and E-test against ticarcillin/clavulanate and ciprofloxacin (kappa < 0.4), by disc diffusion against colistin (kappa < 0.4), and by the Phoenix system against piperacillin/tazobactam (kappa < 0.4). Based on these data, disc diffusion seems to be unreliable for ticarcillin/clavulanate, ciprofloxacin, and colistin; E-test for ticarcillin/clavulanate and ciprofloxacin; and the Phoenix system for piperacillin/tazobactam for S. maltophilia susceptibility testing. Synergistic activity was detected predominantly with TMP-SMX + ticarcillin/clavulanate and TMP-SMX + ceftazidime. TMP-SMX + ceftazidime synergy was also supported by the checkerboard method. However, TMP-SMX + ticarcillin/clavulanate combination revealed indifferent effect by the checkerboard assay. As ticarcillin/clavulanate and ciprofloxacin E-test results were beyond the acceptable correlation limits, synergy testing performed with these agents was considered as unreliable. Further studies are required to standardize susceptibility testing, especially for colistin, ticarcillin/clavulanate, and ciprofloxacin for S. maltophilia. TMP-SMX-containing drug combinations seemed to be more synergistic on multidrug-resistant S. maltophilia; however, these results merit further evaluation.