Parasite testing is generally a difficult proposition. Very few tests seem to yield positive results and many suspect that the majority of people have some form of parasite. I have found that the ParaWellness Research Program led by Dr. Raphael D'Angelo offers parasite testing on both stool and urine that seems to very commonly identify parasites. They then recommend options that can be considered for treatment as well.
I had mine done late last year and identified a couple of protozoa that I have since treated. Whether they are gone or not, I'm not yet clear as I need to do some follow-up testing. I am happy to see that there were not additional parasites detected and have worked to address what was identified.
Their testing conducts multiple microscopic exams on the samples that are submitted and is the only one I have seen that looks at both stool and urine. When you get your test results, they also send a comprehensive reference manual that provide significant additional detail.
UPDATE OCTOBER 2016: At the urging of a darkfield microscopy practitioner, I redid this testing a year after the initial testing was done. This time, we found Giardia and Cryptosporidium. I pursued treatment for both and will do some additional retesting again in the future.
Note: I have no financial relationship with ParaWellness Research.