While Consumer Reports uses customer feedback that can be somewhat subjective but encompassing of the entire car (including elements not necessarily involved with reliability), CarMD can more objectively (in theory) measure a car's reliability with its Vehicle Health Index. The index uses data based on problems associated with check engine codes, as well as the average costs to repair these problems.
In just the second year of its study, CarMD found that Toyota (including Scion and Lexus) has once again held its ground as the most reliable automaker having the fewest issues that would set a check engine light. Likewise, Hyundai stays at the runner up spot. BMW sits in the third spot after not being named to the list at all last year. Honda and Volkswagen round out the top five. In terms of cost to repair, it isn't that surprising that BMW has the most expensive repair costs at an average of $502.48, but we were definitely surprised to see Toyota listed in the two spot with average repairs of $490.72. American automakers General Motors and Ford dropped out of the top five to the eight and nine spots, respectively.
Overall, the most reliable car on the list is the 2010 Toyota Corolla just barely ahead of the 2008 Ford Taurus and the 2008 Toyota Yaris. Of the top 100 cars, 16 of them were Toyotas with Ford following close behind with 15 cars on the list. Ford did take the top spot when it in the truck category and Subaru was named the best in the wagon and crossover SUV category. The study even breaks down the top five causes for a check engine light by automaker.
You can check out the full CarMD reliability study.