I have a six year old whose always been at around the 5th percentile- she's just small for her age, for the most part- what our doctor said to look for is growth- don't focus on the percentile except to see if the growth is going along the same 'curve'- if they are dropping drastically below what was normal for them (so if 5th percentile was normal at birth and they drop to 1st percentile or something like that)- that's when we worry, but if they just grow along the 5th or 3rd percentile all along, it's ok. All people are unique and grow at their own rates- what matters is the growth happens.
Has your son been dropping down the percentile chart or has he been pretty steady at the third percentile? How is he doing with other milestones- any delays?
I have a son like this also. My first born was always in the 90th percentile and my second son was always in the 10th. They are a year apart so it's a good visual of how different kids can be. My smaller son has never been a huge eater but a healthy one. That's really key, keep them eating healthy. Our doctor checks how they are growing based on their own growth curve. My younger son though smaller was always healthy in his growth at each well visit. He's very active and plays a lot of sports and his height hasn't been a factor so far. He's now 12.5 and while his brother is 5 foot 9 inches, he is 5 foot 3 inches. He's not going to be a super tall man but should be within normal. Now, we have two nieces that actually did not have enough human growth hormone determined around 10 years old each. So, if your son falls off his curve, they may choose to check for that but this is pretty rare. Some people are just smaller and it is perfectly normal. And my kids have two grandpas that both were not over 5 foot 7, so the odds were that we'd get at least ONE child who was small in stature. :)) Keep them active in physical activities and eating well and all should be fine! good luck