They found that as animals evolved from walking on four legs to standing up, the so-called neck of the thigh bone - which connects the ball at the top to the rest of the bone - grew broader to support the extra weight.
The study found that the thicker this neck, the more likely that arthritis would develop.
Scientists suggested this could be one reason humans are so vulnerable to hip and knee pain.
They then looked at how human bones would change 4,000 years in the future - and found that the neck of the thigh bone was becoming broader and would lead to more arthritis.
Lead researcher Dr Paul Monk, at the Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, said: 'We see certain things very commonly in hospital clinics - pain in the shoulder with reaching overhead, pain in the front of the knee, arthritis of the hip, and in younger people we see some joints that have a tendency to pop out.
"We wondered how on earth we have ended up with this bizarre arrangement of bones and joints that allows people to have these problems. And it struck us that the way to answer that is to look backwards through evolution."
With a team of scientists, he looked at detailed CT scans - which use X-rays to build a computerised image of inside a body - of 300 ancient specimens from museums.
The team then created 3D models which they used to compare changes in the shape of bones over millions of years.
Predicting how skeletons could change over the next 4,000 years, they warned that we could suffer more problems if our bodies continue to evolve as they have.
Dr Monk said: "What is interesting is if we try and move these trends forward, the (thigh bone) shape that is coming has an even broader neck and we are trending to more arthritis."
He said maintaining good posture and the right physiotherapy could help alleviate the problems caused by human evolution.
Dr Monk added that artificial joints will have to be redesigned in the future to accommodate the evolving shapes of our bones.
The study also found a natural gap in the shoulder through which tendons and blood vessels normally travel has become narrower through evolution.
As this happens, it makes it more difficult for tendons to move. Scientists said it might help explain why some people feel pain when they reach overhead.
Other aches and pains have been linked to evolution. A study last year found people with lower back problems are more likely to have spines like those of chimpanzees.
Professor Mark Collard, of Simon Fraser University in Canada, said: "Our findings show that the vertebrae of humans with disc problems are closer in shape to those of our closest ape relatives, the chimpanzee, than are the vertebrae of humans without disc problems."
