Two problems related to brake master cylinder have been reported for the 2003 Hyundai Sonata. The most recently reported issues are listed below. Please also check out the statistics and reliability analysis of the 2003 Hyundai Sonata based on all problems reported for the 2003 Sonata.
The brake pedal drops during braking with a clunk. The brakes are weak at that point but recover. I replaced the brake pads and rotors and master cylinder, still the same problem. It happens a lot. My wife won't drive the car anymore.
Over the past year, while traveling at various speeds, in various weather conditions my brake pedal very sporadically will not depress. The pedal is solid and will not move/respond for between 1 and recently up to about 6 seconds, which is a lifetime when you are trying to stop a car at 55 mph. Two auto shops have driven the car and can not recreate or diagnose the issue. Based on my own research, I finally resigned to have the master cylinder replaced. However, while the mechanic was replacing the mc he noticed that the vacuum hose had a metal clamp near the mc end and the clamp had shifted down the hose. Inside the hose, where the clamp had been, there appeared to be a spring loaded valve, possibly an internal check valve, which was now "loose" in the hose. It seems that if the clamp is in fact keeping the valve in place and it slowly drifts overtime this problem is something that would only appear with older cars. Also, I've seen reports on internet forums where others have described the same brake problem, however there is no recall listed for this issue. I don't know how many incidents need to be reported before action is taken, but as this is a life-threatening problem I would hope you treat it with urgency and investigate it fully.