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 Minor hiatuses
With the exception of its early years, the first time Homestar Runner went on a hiatus of at least a month was December 2005/January 2006, starting with the release of the Strong Bad Email portrait and ending with the release of the Strong Bad Email highschool.
Homestar Runner again went on hiatus in May/June 2006, after the release of the Strong Bad Email isp. This was due to the birth of a baby to Mike Chapman and Missy Palmer. This hiatus ended with Weclome Back, which also explained what the Homestar Runner characters were up to during that time.
The next hiatus was in December 2006/January 2007, between the releases of Decemberween Short Shorts and looking old, and in July 2007, Matt and Jackie Chapman also gave birth to a baby and stated that Homestar Runner would be taking a break for this reason, although Where's an Egg? was released shortly after this announcement. The next hiatus was in December 2008/January 2009, between the releases of A Death-Defying Decemberween and Hremail 62.
 Strong Bad Emails
The first long Strong Bad Email hiatus was in between email thunder and hremail3184, lasting 280 days (nine months and one week). It was the longest Sbemail gap at the time, and for a while afterwards, one Strong Bad Email came out each month. The last Strong Bad Email, videography, came out on October 5, 2009, and as of now it is the longest Strong Bad Email gap in the history of the site (over 4 years). As of July 24, 2014, the Strong Bad Email hiatus is still ongoing.
During this time, The Brothers Chaps have released drafts for the email that eventually became geddup noise, as well as a calendar that documents the release dates of all Strong Bad Emails and shows an image and a quote from selected emails. In addition, Matt Chapman revealed on his former Twitter page a partial image of scripting for Sbemail 206, which he claimed will be released "when you least expect it".
During 2010, after the April Fools' Day toon Xeriouxly Forxe was released, the first major update in nearly five months, barely any material was produced on the website. Most of the notices presented on the main page were Store offers. This may be because of a new baby in the family, as noted on the FeedBurner page, and the possibility they were busy working on a different project. For the first time in the site's history, no Halloween cartoon was produced in 2010.
After over seven months of no updates, on November 22, Poker Night at the Inventory was released. On December 14, 2010, A Decemberween Mackerel was released, temporarily ending the hiatus. This was shortly followed by Which Ween Costumes? on December 22.
 2011 - 2014
Following the holiday break into the new year, the site was back on hiatus. The only character appearance during 2011 was Puppet Strong Bad appearing at an Aquabats concert in January. Since then, the last site update was a Store offer.
In September, Matt created a Twitter account in which he stated that Homestar Runner would sooner be updated "sporadically and without warning", and that he works for the Nickelodeon program Yo Gabba Gabba, for which he had previously created an animated segment.
December 22, 2011, marked the first time in the site's history that an entire year passed with no new content. On February 27, 2012, Matt posted an out-of-focus image of the apparent script for Strong Bad Email 206 on his Twitter account with the message "Someday, when you least expect it...". He also stated that he works for The Aquabats! Super Show, which, incidentally, was created by the creators of Yo Gabba Gabba; as well as the Disney program Gravity Falls. In January 2013, Matt deleted his Twitter account.
Strong Bad and Homestar Runner made a surprise appearance at W00tstock 5.0 in July 2013, and the Decemberween greeting cards returned to the store around November 23, 2013.
The hiatus was briefly interrupted on April 1, 2014 with April Fools' 2014. At the end of that toon, Strong Bad and Homestar Runner discuss the possibility of there being a substantial amount of time before the next update. This toon replaced the normal welcome screen and remained in place until July.
In July, Matt stated in an interview that he plans to begin updating the website again later in the year.