Without further details I would guess your fits file is using 16 bit signed integers between -32768 and +32767.
In which case you should find that the fits header item called bzero has been set to 32768.
The true integer values are given by your pixel value*bscale + bzero.
This is a very common format for raw data from CCD cameras.
On the other hand if you are talking about processed sky subtracted SDSS images, then of course some pixels are negative - the average pixel in a "sky" region will be zero, so a substantial fraction must be negative.
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