First, I want to get out of the way that the equivalence principle, which is well supported by experiment, contends that gravity and acceleration are one in the same: "pseudo"-gravity caused by acceleration is equivalent to "real" gravity. So, there is no physical difference between walking in a spacecraft accelerating at 9.81 m/s2 and walking on the surface of the Earth. Therefore, there can be no difference in the biological effects. The body cannot know the difference.
But you asked about a rotating space station. A rotating station isn't exactly the same as a uniformly accelerating spacecraft. In a rotating station, a centripetal acceleration is constantly applied to keep going around the circle. In the rotating reference frame, this centripetal acceleration appears as centrifugal force, which acts as a replacement for gravity. By the equivalence principle, the effect of the centripetal acceleration (or centrifugal force) is identical to a gravitational force. However, the necessary centripetal acceleration to keep you going in a circle depends on your distance from the rotation axis. Because of this, any movement that changes your distance from the axis (say, bending over) will result in observation of the Coriolis force in the rotating frame. For small rotating space stations, the Coriolis force will cause dizziness, motion sickness and weird trajectories for dropped and thrown objects (presumably affecting O'Neill cylinder baseball).
The only physical difference between the rotating cylinder and real gravity is the Coriolis effect. So, any biological differences between real gravity and artificial gravity must be caused by the Coriolis effect. (I'm assuming that the rate of rotation of the cylinder is nearly uniform so that the Euler force is nearly zero).
The Coriolis acceleration depends only on the rate of rotation of the cylinder and your velocity, $\mathbf{a_\mathrm{Coriolis}}=2 \mathbf{v} \times \mathbf{\Omega}$, where $\mathbf{\Omega}$ is the angular velocity. On the other hand, as the radius of your cylinder gets larger, the rate of rotation required to attain Earth-like artificial gravity is reduced, because the apparent acceleration is $|a_\mathrm{centrifugal}| = \omega^2 r$, where $r$ is the radius of the cylinder. So, the bigger the radius of the cylinder, the less the Coriolis effect for a fixed centrifugal acceleration (for instance, 9.81 m/s2).
The question of how big the cylinder has to be to not cause dizziness has been addressed on WorldBuilding. It looks like it needs to be at least a few hundred meters in radius for 1 g acceleration. There may be other subtle biological effects at smaller Coriolis effects that we don't yet know about, but our bodies are made to move around, so at some point the small Coriolis effects must become negligible. As the size of the cylinder increases, the "artificial" gravity comes closer and closer to being physically equivalent to Earth's gravity. Indeed, the Earth itself has some Coriolis acceleration due to $\Omega = 2 \pi / \mathrm{day}$.
A nice discussion of the topic of artificial gravity is provided by Theodore Hall.
Edit: As pointed out by BlueCoder, the gradient of the effective gravitational field of a spinning structure on the one-kilometer-scale would be significantly larger than on Earth and could also be perceptible. This is described in the Theodore Hall link above as a "head-to-foot acceleration gradient". Too large a gradient gives "sensations of heaviness in the feet and lightness in the head". For a fixed effective gravitational acceleration, this gradient would be inversely proportional to the radius of the floor of the habitat.
