Most of the Third Subdivision came into being as the Mississippi & Missouri, after they completed the Davenport to Iowa City segment in 1855. Progress was slow, however, and by the end of 1865, a decade later, the line only reached Kellogg. With the Civil War drawing to a close and the so-called Transcontinental Railroad being built west from Omaha, the Chicago & Rock Island could wait on the M&M no more. They purchased the line in 1866, had it extended to Des Moines by 1867, and completed into Council Bluffs by 11-May-1869, a day after the Transcontinental is completed in Utah. The line became part of the core Rock Island system over time, providing a connection to the Union Pacific mainline at Omaha as well as providing the shortest connection to the Nebraska, Kansas, and Colorado parts of the Rock system. The line fell into bankruptcy in 1980, between 1981 and 1984 was operated by the Iowa Railroad, and in 1984 was sold to Heartland Corp, who subsequently created Iowa Interstate to operate it.

In the Iowa Interstate era, two major changes have occurred with the route. The first was the Newton yard relocation. Originally located near the heart of town, it was moved out to the northeastern edge sometime in the late 1990s (1997?). This was done to make room for Maytag expansion for their new corporate headquarters and additional parking. The new yard includes the new Lee Horst Transportation Center, which in addition to providing intermodal services, also includes a small shop facility. The facility is named in honor of Lee Horst, a former General Road Foreman on IAIS and career railroad man who passed on in 2002.

Secondly, the connection between the IAIS mainline and the CRANDIC line (former Milwaukee line) near Homestead was rebuilt to have an eastern leg, forming a wye. Placed into service 11-Feb-2000, this formerly seldom-used junction was re-christened Yocum Connection, in honor of Fred Yocum, a former president of IAIS. This is now the major interchange point between IAIS and the CRANDIC, eliminating most of the need for the hill track in Iowa City. It also worked out well for the new ICCR/CRIC trains, which can run straight through the junction without any sort of runaround to get lined up.

Today's operations on the Third Sub include the two mainline trains - CBBI and BICB - as well as daily sets of ICCR/CRIC interchange trains. CBBI generally starts the day in Newton, switching and preparing for the run east. Somewhere in the late morning, it departs Newton eastbound. On the other end of the sub, RIIC (Rock Island - Iowa City, off the First Sub) is the first into Iowa City in the mornings. It switches out what it needs to and proceeds west as ICCR (Iowa City - Cedar Rapids) sometime around 1000h-1200h. Behind it, BICB typically arrives in Iowa City around noon (though this varies significantly). ICCR proceeds west, turning north onto the Crandic line at Yocum Connection, often meeting the eastbound CBBI there. By this time, BICB is usually done at Iowa City, and either holds for CBBI in the yard, or proceeds west and meets BICB somewhere en route. CBBI pulls into Iowa City and works the yard in the mid to late afternoon, and BICB pulls into Newton in the late afternoon or evening. Meanwhile, once ICCR completes its work at the Cedar Rapids interchange, it works back down to Yocum and heads back east into Iowa City, where it comes in usually after the CBBI has completed its work and departed east. Thrown into this mix are also the Newton Switcher that works industries in and around Newton, and the Iowa City switcher, which runs pretty much anywhere between Marengo and Wilton.

IOWA INTERSTATE RAILROAD - THIRD SUBDIVISION IOWA CITY, IA, TO NEWTON, IA Maximum Speed: 40 MPH Length: 85.7 miles Entire line Track Warrant Control Radio: IAIS - 161.220 MHz and 160.305 MHz
	Mile Post	Station	Sidings	Other Tracks		Notes
W E S T B O U N D	114.2	Bureau, IL	5290	Yes	E A S T B O U N D	Junction with Subdivision 1
	236.8	Iowa City, IA	10000	Yes		Junction with Subdivision 1 CRANDIC interchange
	241.0	Vernon		Yes		Near Coralville Mall
	242.7	Hawkeye	1270	Yes
	244.6	Tiffin				MP approximate, not official IAIS station
	~248.5	Detector				MP approximate, detector not yet operational
	251.5	Oxford		Yes
	256.6	Homestead	2995
	259.0	Yocum Connection		Yes		Formerly Crandic Junction Connection to CRANDIC line to Cedar Rapids
	262.1	South Amana				MP approximate, not official IAIS station
	267.3	Marengo	5330	Yes
	273.9	Ladora		Yes
	279.9	Victor		Yes
	287.7	Brooklyn	7835	Yes
	293.7	Malcom		Yes
	297.3	Ascalon
	302.7	Grinnell	4110	Yes		UP Crossing
	313.8	Kellogg	3955	Yes
	322.5	Newton, IA	6100	Yes		Junction with Subdivision 4

Timetable Legend:

On 1 Sep 2010, IAIS assumed dispatching of the CRANDIC Third Sub from Yocum Connection (milepost 21.8) to Fairfax (milepost 8.l). This line was deemed IAIS Subdivision 3B.

IOWA INTERSTATE RAILROAD - SUBDIVISION 3B YOCUM CONNECTION, IA, TO FAIRFAX, IA Maximum Speed: Unknown Length: 8.1 miles Entire line Track Warrant Control Radio: IAIS - 161.220 MHz and 160.305 MHz Radio: CIC - 161.055 MHz and 160.500 MHz
	Mile Post	Station	Sidings	Other Tracks		Notes
W E S T B O U N D	8.1	Fairfax			E A S T B O U N D	North end of IAIS Sub 3B Connection with CRANDIC Third Sub
	11.6	Walford
	17.1	East Amana				MP approximate - not on CIC timetable
	18.4	Amana
	19.7	Amana Refrigeration
	21.8	Yocum Connection				Junction with IAIS Subdivision 3 Became IAIS Sub 3B Sep 2010

Timetable Legend: