The short answer: while there is no clear evidence as yet directly linking bedroom usage of mobile phones to specific health issues, there are reasons why it might not be a good idea for your overall health regardless.
The long answer: to date, the evidence that mobile phones cause health problems (cancer being the most frequently cited risk) is inconclusive. A review of studies by the International Agency for Research on Cancer concluded that RF-EMF transmissions were "possibly carcinogenic", which is a fairly qualified response. There certainly hasn't been enough research to definitively state it's not a problem, especially since mobile phones as a widespread phenomenon are (in medical terms) a relatively recent development. However, those studies which have been conducted don't suggest any clear evidence of a sustained health risk.
What's worth noting in this context is that any risk that does exist is much higher if you're actually holding the phone to your head. Standard risk minimisation advice in this field is to use a hands-free kit. As such, if your phone is residing near to your bed purely to serve as an alarm, the potential risk is minimal. If you put your phone into flight mode, so that it's not attempting to use either mobile or Wi-Fi networks, it's essentially zero.
With all that said, however, there is one very good health reason not to have a bedside mobile phone: it's likely to play havoc with your sleep patterns. We've written before about how using electronic devices immediately before sleeping can make it much harder to get a good night's sleep, since the bright screen inhibits the production of melatonin and places the brain ina more alert mode. Phones definitely fall into the 'bad' category in this regard, along with computers and TVs (non-backlit ebook readers such as the Kindle are OK).
Not keeping your phone by your bed makes it less likely you'll decide to indulge in a quick bout of gaming, social networking or web browsing right before you go to sleep. If you're disciplined enough to simply dock your phone and sleep, good on you, but discipline is a quality found in widely varying quantities. For many of us, removing temptation is the best bet.
A final thought: relationships always involve compromise. The health risks of having a mobile in the bedroom might be minimal, but if your partner feels strongly about it, there doesn't seem to be a compelling reason to take a stand on the issue. You can still enjoy your phone in the rest of the house.
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