Gina Kolata has an article in the New York Times about how long it takes to recover after a marathon. As she points out, marathons stress many different systems in your body, each of which recovers at a different rate -- glycogen stores, muscle soreness, mental fatigue, and so on. The verdict: nobody really knows how long it takes, though many studies seem to show a return to something approximating full strength after about a week.
The funny thing is, despite these findings, no one would recommend that you tackle another all-out marathon a week -- or even a month -- later. Anyone who has run a marathon knows intuitively that these studies aren't the full story. One possibility is the role of the mind, as Tim Noakes tells Kolata:
So Dr. Noakes relies on the experience of great runners, who tell him that there is a large psychological component to recovery. Many elite marathoners run only one or two races a year. After a marathon, he said, it “probably takes at least six months for the mind to recover fully.”
I'll suggest another possible component: neuromuscular fatigue. When you decide to contract your leg muscle, your brain sends a signal that travels down your spinal cord and eventually reaches the muscle, where muscle fibers contract in response. There's no doubt that running a marathon -- particularly on hilly terrain -- will damage some of the muscle fibers themselves. This is what will result in soreness for the next few days. But even after that soreness is gone, you may not be back to full strength when you try to contract your muscles, because the signal from your brain gets disrupted somewhere before it gets to the muscle -- this is "neuromuscular" fatigue.
A Danish study in 2007 tested the muscular and neuromuscular characteristics of eight marathoners after a race (average time: 2:34:40). Five days later, the runners' maximum voluntary muscular contraction was still reduced compared to pre-race values even though the contractile properties of the muscle itself were back to normal, suggesting that the loss of strength was neuromuscular. Another study, published last year, studied 11 finishers of an extreme mountainous 100-miler: 16 days after the race, most muscle measurements had (surprisingly!) returned to normal, but a couple of measurements ("potentiated twitch" and "potentiation") were still suppressed.
Bottom line: even once you're feeling fine a week or so after the marathon, there may be lingering effects in your body, particularly if you've really gone to the well. We don't know exactly what these factors are -- but if I had a hypothetical all-powerful physiological measurement tool, I'd bet it would still be able to find some markers of fatigue or damage two week