My puppy is 15 weeks old and has just taken his first does of heartgard from the vet (have only had him for about 7 weeks and I'm not sure what the breeders gave him) and upon the first dose he threw up within about a half an hour. Called the vet the next day and they told me that I should give him another dose and that he would be fine since the doses are so low that he could eat a whole package and be OK. So the following day (tue - 1st dose , thur - 2nd dose) he was given another dose and within an hour he was acting out of nature. Within about 2 hours of his dose he had severe diarrhea. All night I stayed up with him to let him out. Sometimes he had to and sometimes he thought he did. The following morning I found an accident (between 5 am and 7:30 am) and this time it had blood. Worried that it was getting extremely serious I took him to the vet by 8am. They said it couldn't be the heartgard and that it had to be something else and sent us home with IAMS low residue canned food and meds (Loperamide 2mg capsules for diarrhea and Flagyl/Metronidazole 250mg tablets as an antibiotic). The vet gave me an explanation that it was probably his food and that after 3 days of his antibiotic and low residue diet that I could start to mix his food in and he should most likely be OK. I don't think his food is to blame as he was perfectly fine before his dose of heartgard and spiraled after the second dose of it. Am I right and what can I do to get my poor puppy feeling better. He's still up and down with his behavior and although he doesn't have diarrhea (due to his anti-diarrhea med) he's not his usual lovey self. Any ideas. Should I take him to another vet to get a second opinion? Did the heartgard cause some serious damage?

As a rule heartguard is very safe when given as directed by the manufacturer. For what it is worth I have not heard this complaint where I work, but vomiting and diarrhea have been reported as side effects according to the listed information here.
http://heartguard.com/pdf/HEARTGARD-Chewables-for-Dogs.pdf

That being said, I would ask if your pup is up to date on all of his vaccines and deworming. You seem to be very intuitive about his care, but in my life I have learned never to assume anything.
I would also ask if the vet did a diagnostic fecal exam to check for intestinal parasites?

In regards to heartworm prevention, there are other alternatives including topical products, if it is decided that he is sensitive to something in the heartguard.

Whether to get a second opinion, that is entirely your call.
If you are not satisfied with the answers you are getting from your vet, that is certainly a valid option.

Thank you for your response. My puppy is up on all of his shots and has been tested for parasites. I took a stool sample with me to the vet the first appointment and had it tested and it came back clean. Hes been eating a bland food diet for three days now and hasn't had any more diarrhea. I went out and picked up some sensitive stomach puppy food and will continue to work with him back into kibble from soft food.

Thanks for the update, I'm glad to hear your pup is doing better.