I purchased a Steripen handheld UV water purifier. It uses UV light to treat water that may be contaminated. The claim is that the UV radiation damages the microorganism in a way that prevents reproduction, and that microbes that can't reproduce can't make you sick. 

But from my memory of Microbiology class many years ago, I recall that some bacteria release endotoxins that cause illness.

So I'm thinking that even if I used this device on a glass of lake water that had a significant amount of bacteria, they still might dump endotoxins into my system if the cells are lysed in my stomach acid.

Any thoughts on this?

Thanks!

You are not wrong and it depends on the water source. UV serves a similar purpose as chlorination. However, if the water is already  highly contaminated it may still be unsafe (including e.g. neurotoxins from algae blooms).

I looked into this, then forgot about it. You need something like a microporous polyethylene membrane to filter it out.

In principle, enough UV of short enough wavelength will destroy almost  any organic molecules in the water.

You are not going to achieve that with anything you can carry in a pocket.

We're constantly exposed to endotoxin -  including drinking water and via normal gut and oral flora.    High levels in drinking water have been associated with cyanobacterial blooms. Hemodialysis and respiratory exposure to endotoxin-laden water has been associated with some symptoms - not drinking the water.  I'd not be worried about the water mentioned above and wouldn't put too much faith in the device.   UV doesn;t penetrate water that well and even less in water with suspended particulates.  Also be aware that microorganisms use both light and dark repair mechanisms to repairr UV damage.