I'm using a modified version of some of the example code available from Atmel for my project, but I need to use the malloc function now.

What is the best way of getting this implemented on the AT91SAM3U4?

Hi!
Isn't it declared in stdlib.h? Remeber to reserve memory in the heap by an appropriate entry in the scatter file.

...
ARM_LIB_HEAP 0x76FFD000 EMPTY 0x20000 {
}

ARM_LIB_STACK 0x76000000 EMPTY -0x2000 {
}
...

The problem I get from compiling is that _sbrk is undefined.

Hi!
I haven't experienced the problem. Could you have a look at:
http://embdev.net/topic/129753
http://embdev.net/topic/152798
That the only thing I can help you

The _sbrk() function is a system call, which enlarges an already allocated memory block.

You should really think long and hard before pulling in these OS stuff. The whole malloc() idea (or new in C++) originates from larger systems with virtual memory and MMU. This is an environment were you assumed not to know anything of actual addresses - things which are essential in this kind of embedded systems.

Are you ready to handle out-of-memory events at runtime on your Cortex M3 application ?

If you can get away with a roll-your-own, static memory allocation, you probably spare yourself a lot of hassle.