If you plan to go in July or August it will be very hot in the afternoon. Also, the morning will be less crowded. Most organized tours will not yet have arrived if you get there early enough.

We will be there in late May...

Since you will have already stayed in Rethymno, i presume that you will have covered all nearby attractions and nice places ( as per my previous posts).

On the way to Heraklion, you can stop at the Kournas Lake ( very near to Georgioupolis), the only natural lake of Crete.

Another stop could be Fodele, a small village where the famous painter Dominikos Theotokopoulos ( El Greco) is supposed to be born.
There isn't anything else on the way after rethymnon, that could be of interest.... perhaps a short break in Agia Pelagia for a coffee....

If you have enough time though, you could drive to Agios Nikolaos , which is only 60 km east of Heraklion. ( 1 hour driving time max.)

Even in late May if the sky is clear and there's no wind it can be very hot.

Thank you all! !

Absa! I've done it- 7am from Chania and it's a far better time to be on the road too.

A lot of the site is unshaded. It can be blazingly hot.

I think you need to count at least 2 hours. Both times I've done it, I've twinned it with a visit to the National Museum but I think it's still closed for renovations, although there's a temporary exhibit. I've always found that to be a long enough day without other stops

Thanx Sheila - sounds good. That way the pool at our hotel will feel really nice afterwards!

For what it's worth the temporary exhibit of the museum is still very impressive.

I, too, would do it in the morning. 4 pm is too late.

I saw the temporary exhibit this summer and, yes, it was very impressive. My impression is that they have selected the best items to display.

We took a guided tour once we got there. It was 20 euros per adult and free for children. I don't remember the name of the guide, a short woman in her 60s, but she was very very good. If there is a tour, I recommend to take it.

It's been "temporary" for about 6 years now.

The museum, which is the most important of it's kind in the world regarding Minoan art, is closed since 2006 due to renovations, that seem to be endless....

Unfortunately from the 12.000 exhibits of the old museum, one can only see 500 now ( the highlights), and only 25 persons have access to the little room at the same time.

There has been a huge delay in the renovation of the museum but according to the newest schedule the museum is expected to open it's gates in September 2013, however it is possible that they will open hall A and B in the next two months, due to a huge pressure of the local society.

The museum is the most important local attraction of the ( not so beautiful) city of Heraklion, along with Knossos,

Yes, do take the guided tour. The second time we only used the Blue Guide and it was fine, but we'd have got a lot less out of it without having had the guide the first time.

Knossos was closed at 3pm the day we were there. I believe it was May 5th. It could be because it was election weekend. I was disappointed needlesss to say.
Things in Greece change all the time, sometime to your benefit, other times not.